Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

The Ensembl computing architecture.

James A Cuff1, Guy M P Coates, Tim J R Cutts

  • 1The Broad Institute, Cambridge, Massachusetts 02141, USA. jcuff@broad.mit.edu

Genome Research
|May 5, 2004
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

An Assessment of Anki Flashcards Use in Comparison to Alternative Study Methodologies in First Year Graduate Entry Medical Students.

Medical science educator·2026
Same author

An overview of Ensembl.

Genome research·2004
Same author

Application of high-throughput computing in bioinformatics.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences·2003
Same journal

A unified analysis of cell type- and trajectory-associated pathways in single-cell data using Phoenix.

Genome research·2026
Same journal

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin.

Genome research·2026
Same journal

Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.

Genome research·2026
Same journal

Spatially informed reference-free cell-type deconvolution for spatial transcriptomics with SpatialCD.

Genome research·2026
Same journal

Spatially resolved profiling of steroid nuclear receptors reveals a role for the disordered N-terminal domains in genome targeting and AP-1 interaction.

Genome research·2026
Same journal

Flexible and scalable inference of spatially varying correlation in spatial transcriptomics with spCorr.

Genome research·2026
See all related articles

Building large-scale eukaryotic genome annotation systems requires careful planning. This study details essential considerations for designing high-performance computing farms, highlighting successful and unsuccessful strategies to avoid common pitfalls.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The Ensembl project automates the annotation of large eukaryotic genomes.
  • Automated genome annotation demands significant computational resources due to extensive sequence comparisons.
  • Traditional supercomputing is costly; therefore, distributed computing farms are increasingly utilized.

Purpose of the Study:

  • To define and explain essential elements for designing large-scale biocompute systems.
  • To provide insights into potential pitfalls in implementing high-performance computing farms.
  • To guide readers undertaking large-scale biocompute projects.

Main Methods:

  • Analysis of server architecture and network infrastructure for distributed computing farms.

Related Experiment Videos

  • Evaluation of implemented solutions, detailing successes and failures.
  • Focus on practical considerations for building and managing hundreds of compute nodes.

    • Main Results:

    • Identification of critical factors in designing complex, multi-node computing farms.
    • Documentation of specific architectural and infrastructural solutions that proved effective.
    • Case studies of failed implementations and their consequences.

    Conclusions:

    • Successful implementation of large-scale biocompute projects relies on robust server architecture and network design.
    • Learning from both successful and failed strategies is crucial for efficient resource utilization and project completion.
    • This study offers practical guidance to mitigate risks in deploying high-performance computing infrastructure for genome annotation.